ELIXIR (https://www.elixir-europe.org) unites Europe’s leading life science organisations in managing the increasing volume of data being generated by publicly funded research. ELIXIR operates in a Hub-Node model with the Hub coordinating the activities undertaken by the Nodes via five technical platforms: Compute, Data, Interoperability, Tools, and Training to build a sustainable and foundational framework for Life Science informatics communities. This is done by establishing strategic guidelines underlying scientific operations across ELIXIR’s twenty-one Node members (as of May 2018). The ELIXIR Interoperability Platform (EIP) has been established to deal with the challenge of delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data across the different levels of complexity and variety of life science data types: across the datasets, data catalogues, data tools and services; across the multitude of biological disciplines and geographical or organisational boundaries. The EIP aims to make available the services and resources needed to make data FAIR. These strategies will be founded on FAIR Principles. Ontologies are a crucial component of the EIP strategy, with OBO Foundry Ontologies recognised as reference resource, and leveraged through resources such as Ontology Lookup Service, which provides additional user services for search and annotation. EIP is currently engaged in addressing specific community-derived use cases where incorporating ontological information is essential: rare disease, marine metagenomics, and plant informatics. These require reference ontologies such as Human Phenotype Ontology (HP), Disease Ontology (DO), Cell Ontology (CL), and UBERON.